A new version of the stand-alone applications is available.
Users are encouraged to use the BLAST+ applications available at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ This release includes a substantial number of bug fixes and new features for the BLAST+ applications.
Improvements:
* Enhanced documentation, includes simplified setup instructions, available at http://www.ncbi.nlm.nih.gov/books/NBK1762
* Added support for hard-masking of BLAST databases.
* Improve performance of makeblastdb for FASTA input with large numbers of sequences, improve error checking.
* Allow Best Hit options and XML formatting for Blast2Sequences mode
* Allow multiple query sequences for psiblast.
* Allow specification of any multiple sequence alignment sequence as the master with the -in_msa psiblast argument.
* Add an optional -input_type argument to makeblastdb.
* Added support for query and subject length to tabular output.
* Performance of -seqidlist argument improved.
* The minimum of the number of descriptions and alignments is now used for tabular and XML output (consistent with the behavior of the older blastall applications).
Bug fixes:
* Makeblastdb and blastdbcmd problems with parsing, storing, and retrieving sequence identifiers.
* Missing subject identifiers in tabular output.
* Blast_formatter ignoring -num_alignments and -num_descriptions
* Blast archive format could be saved incorrectly with multiple queries.
* Blast_formatter established an unneeded network connection.
* Blast_formatter did not save masking information correctly.
* Rpstblastn might crash if searching many sequences.
* Indexed megablast would not run in multi-threaded mode.
* Query title in the PSSM saved by psiblast was not being stored.
* Possible failure to run in multi-threaded mode with multiple queries or large database sequences.
* Tblastn runs with database masking might miss matches.
* Truncated output for sequence input with extra spaces in the defline
* Problem with MacOSX binaries on MacOSX 10.5
BLAST+ applications, as well as the legacy C applications (e.g. blastall), may be downloaded from http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
Users are encouraged to use the BLAST+ applications available at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ This release includes a substantial number of bug fixes and new features for the BLAST+ applications.
Improvements:
* Enhanced documentation, includes simplified setup instructions, available at http://www.ncbi.nlm.nih.gov/books/NBK1762
* Added support for hard-masking of BLAST databases.
* Improve performance of makeblastdb for FASTA input with large numbers of sequences, improve error checking.
* Allow Best Hit options and XML formatting for Blast2Sequences mode
* Allow multiple query sequences for psiblast.
* Allow specification of any multiple sequence alignment sequence as the master with the -in_msa psiblast argument.
* Add an optional -input_type argument to makeblastdb.
* Added support for query and subject length to tabular output.
* Performance of -seqidlist argument improved.
* The minimum of the number of descriptions and alignments is now used for tabular and XML output (consistent with the behavior of the older blastall applications).
Bug fixes:
* Makeblastdb and blastdbcmd problems with parsing, storing, and retrieving sequence identifiers.
* Missing subject identifiers in tabular output.
* Blast_formatter ignoring -num_alignments and -num_descriptions
* Blast archive format could be saved incorrectly with multiple queries.
* Blast_formatter established an unneeded network connection.
* Blast_formatter did not save masking information correctly.
* Rpstblastn might crash if searching many sequences.
* Indexed megablast would not run in multi-threaded mode.
* Query title in the PSSM saved by psiblast was not being stored.
* Possible failure to run in multi-threaded mode with multiple queries or large database sequences.
* Tblastn runs with database masking might miss matches.
* Truncated output for sequence input with extra spaces in the defline
* Problem with MacOSX binaries on MacOSX 10.5
BLAST+ applications, as well as the legacy C applications (e.g. blastall), may be downloaded from http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download